chr6-30110458-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_007028.5(TRIM31):c.734A>G(p.Gln245Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00164 in 1,614,156 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q245P) has been classified as Uncertain significance.
Frequency
Consequence
NM_007028.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM31 | NM_007028.5 | c.734A>G | p.Gln245Arg | missense_variant | 4/9 | ENST00000376734.4 | |
TRIM31-AS1 | NR_126470.1 | n.274-1260T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM31 | ENST00000376734.4 | c.734A>G | p.Gln245Arg | missense_variant | 4/9 | 5 | NM_007028.5 | P1 | |
TRIM31-AS1 | ENST00000440874.1 | n.274-1260T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
TRIM31 | ENST00000480808.1 | n.280A>G | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
TRIM31 | ENST00000485864.5 | n.424A>G | non_coding_transcript_exon_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00802 AC: 1221AN: 152190Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00247 AC: 622AN: 251418Hom.: 8 AF XY: 0.00200 AC XY: 272AN XY: 135880
GnomAD4 exome AF: 0.000967 AC: 1414AN: 1461848Hom.: 18 Cov.: 31 AF XY: 0.000877 AC XY: 638AN XY: 727218
GnomAD4 genome ? AF: 0.00805 AC: 1226AN: 152308Hom.: 8 Cov.: 32 AF XY: 0.00801 AC XY: 597AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at